In total there are eight nations from which to choose from in Rise of Civilizations and each offers their own bonuses which you need to consider carefully as they are more important than the commanders the nation starts with.
At the start of the game none of the nations has a particularly good commander, you will eventually unlock better ones as you progress and therefore have more options. All commanders are available to be unlocked by all nations but your bonuses and unique troops are specific to the civilization you chose.
The best overal nation is probably Germany due to its troop taining boost and faster Action point recovery. You may want to also consider Spain and Rome as one allows you to collect resources quicker than the other nations, while the other has increased marching speed. None of the nations bonuses really overpower when compared to another so even if you choose one based on personal preferences and not it's bonuses you will not be at a large disadvantage.
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